1. Field of the Invention
The invention relates generally to screening assays and molecular medicine, and more specifically to methods for identifying individuals having or at risk of developing cancer, for grading the severity and determining the prognosis of such cancers, and for treating or preventing such cancers.
2. Background Information
Lung cancer is the leading cause of cancer death, and 80% of lung cancers are non-small cell lung cancer (NSCLC). While human lung cancer is not thought of as a genetic disease, a variety of molecular genetic studies have shown that lung cancer cells have acquired a number of genetic lesions including activation of dominant oncogenes and inactivation of tumor suppressor or recessive oncogenes. In fact, it appears that to become clinically evident, lung cancer cells have to accumulate a large number (perhaps 10 or more) of such lesions. For the dominant oncogenes, these include point mutations in the coding regions of the ras family of oncogenes (particularly in the K-ras gene in adenocarcinoma of the lung) and amplification, rearrangements, and/or loss of transcriptional control of myc family oncogenes (c-, N-, and L-myc), with changes in c-myc found in non-small cell cancers while changes in all myc family members are found in small cell lung cancer. Tumor mutations in ras genes are associated with poor prognosis in non-small cell lung cancer, while tumor amplification of c-myc is associated with poor prognosis in small cell lung cancer.
For the recessive oncogenes (tumor suppressor genes), cytogenetic and restriction fragment length polymorphism (RFLP) analyses have shown deletions (allele loss) involving chromosome regions 1p, 1q, 3p14, 3p21, 3p24-25, 3q, 5q (familial polyposis gene cluster), 9p (interferon gene cluster), 11p, 13q14 (retinoblastoma, rb, gene) 16q, and 17p13 (p53 gene), as well as other sites. There appear to be several candidate recessive oncogenes on chromosome 11q that are involved in nearly all lung cancers.
The large number of genetic lesions in clinically evident lung cancer has prompted a search for these mutations in lung tissue before classic cytopathologic evidence of malignancy can be found, to provide for molecular early diagnosis and as intermediate endpoints in prevention efforts, including chemo-prevention treatment.
Pancreatic cancer is the fourth leading cause of cancer death in men and in women and each year ˜28,000 Americans die of the disease (6). Frequent genetic changes such as mutational activation of the K-ras oncogene and inactivation of the p16, DPC4, p53, MKK4, STK11, TGFBR2, and TGFBR1 tumor suppressor genes have been described in pancreatic cancer (7, 8). Although multiple tumor suppressor pathways have been shown to play a role in pancreatic carcinogenesis, little is known about the contribution of DNA methylation to inactivation of genes in these pathways. Recently, a novel technique, methylated CpG island amplification (MCA), was developed to enrich for methylated CpG rich sequences. MCA coupled with RDA (MCA/RDA) can recover CpG islands differentially methylated in cancer cells.
Primary hepatocellular carcinoma is one of the most common tumors in the world. It is especially prevalent in regions of Asia and sub-Saharan Africa, where the annual incidence is up to 500 cases per 1000,000 population. In the United States and western Europe, it is much less common, accounting for only 1 to 2 percent of malignant tumors at autopsy. Hepatocellular carcinoma is up to four times for common in men than in women and usually arises in a cirrhotic liver.
The principal reason for the high incidence of hepatocellular carcinoma in parts of Asia and Africa is the frequency of chronic infection with hepatitis B virus (HBV) and hepatitis C virus (HBC). These chronic infections frequently lead to chirrhosis, which itself is an important risk factor for hepatocellular cancinomas. In patients with HBV infection and hepatocellular carcinoma, there can be modifications of cellular gene expression by insertional mutagenesis, chromosomal rearrangements, or the transcriptional transactivating activity of the X and the pre-52/S regions of the HBV genome. These alternations probably occur during the process of liver cell injury and repair.
Thus, there is a need in the art for new and better methods for diagnosing individuals having or at risk of developing lung, liver and pancreatic cancers as well as a need for methods of treatment of such conditions.